Title: Algebraic Statistics Applications in Epidemiology



Abstract: Interactions between single nucleotide polymorphisms (SNPs) and complex diseases have been an important topic throughout epidemiological studies. Previous studies have mostly focused on gene variables at a single locus. In this talk, I will discuss a focused candidate gene study to test the interaction of multiple SNPs with the risk of different types of cancer.

We will exemplify the fact that traditional asympotic results in statistical analysis do not apply in our setting. This is due mainly to the fact that we have a relatively small fixed data set.  In our work we develop a new statistical approach using techniques from the field of algebraic statistics. Algebraic statistics focuses on mathematical aspects of statistical models, where algebraic, geometric and combinatorial insights can be useful to study behavior of statistical procedures.



Using the R package algstat, developed by Kahle, Garcia Puente, and Yoshida, we implemented an algebraic statistics method that can test for independence between several variables and the desease. We applied our methods to the study of gene-gene interaction on cancer data obtained from the European case-control study Gen-Air extending previous work by Ricceri, Fassino, Matullo, Roggero, Torrente, Vineis, and Terracini.

Title: Structural and Functional Characterization of Expected and Aberrant Metal Ion Coordination in Proteins

Abstract: Metalloproteins bind and utilize metal ions for a variety of biological purposes.   Due to the ubiquity of metalloprotein involvement throughout these processes across all domains of life, how proteins coordinate metal ions for different biochemical functions is of great relevance to understanding the implementation of these biological processes. Towards these ends, we have improved our methodology for structurally and functionally characterizing metal binding sites in metalloproteins.  Our new ligand detection method is statistically much more robust, producing estimated false positive and false negative rates of ~0.11% and ~1.2%, respectively.  Additional improvements expand both the range of metal ions and their coordination number that can be effectively analyzed.  Also, the inclusion of many additional quality control filters has significantly improved structure-function Spearman correlations as demonstrated by rho values greater than 0.90 for several metal coordination analyses and even one rho value above 0.95.     Also, improvements in bond-length distributions have revealed bond-length modes specific to chemical functional groups involved in multidentation.  Using these improved methods, we analyzed all single metal ion binding sites with Zn, Mg, Ca, Fe, and Na ions in wwPDB, producing statistically rigorous results supporting the existence of both a significant number of unexpected compressed angles and subsequent aberrant metal ion coordination geometries (CGs) within structurally known metalloproteins.  By recognizing these aberrant CGs in our clustering analyses, high correlations are achieved between structural and functional descriptions of metal ion coordination.  Moreover, distinct biochemical functions are associated with aberrant CGs versus non-aberrant CGs.

TITLE: Synchrony in a Boolean network model of the L-arabinose operon



ABSTRACT: In genetics, an operon is a segment of DNA that contains several co-transcribed genes, which together form a functional regulatory unit. Operons have primarily been studied in prokaryotes, with both the lactose and tryptophan operons in E. Coli having been classically modeled with differential equations and more recently, with Boolean networks. The L-arabinose operon in E. coli encodes proteins that function in the catabolism of arabinose. This operon has several complex features, such as a protein that acts both as an activator, a DNA looping repressing mechanism, and the lack of inducer exclusion by glucose. In this talk, I will propose a Boolean network model of the ara operon, and then show how computational algebra in Sage establishes that for 11 of the 12 choices of initial conditions, the state space contains a single fixed point that correctly predicts the biology. The final initial condition describes the case where there are medium levels of arabinose and no glucose, and it successfully predicts bistability of the system. Finally, I will compare the state space under synchronous and asynchronous update, and show how the former has several artificial cycles that go away under a general asynchronous update.

Title: Insight into Molecular through Subcellular Calcium Signaling via Multi-Scale Simulation

Abstract: Calcium is critical to a wide range of physiological processes, including neurological function, immune responses, and muscle contraction. Calcium-dependent signaling pathways enlist a variety of proteins and channels that must rapidly and selectively bind calcium against thousand-fold higher cationic concentrations. Frequently these pathways further require the co-localization of these proteins within specialized subcellular structures to function properly. Our lab has developed multi-scale simulation tools to elucidate how protein structure and co-localization facilitate intracellular calcium signaling. Developments include combining molecular simulations with a statistical mechanical model of ion binding, a homogenization theory to upscale molecular interactions into micron-scale diffusion models, and reaction-diffusion simulations that leverage sub-micron microscopy data. In this seminar, I will describe these tools and their applications toward molecular mechanisms of calcium-selective recognition and cross-talk between co-localized calcium binding proteins inside the cell.

Title: Qualitative Assesment of the Role of Temperature Variations on Malaria Transmission Dynamics

Speaker: Folashade B. Agusto, Department of Ecology and Evolutionary Biology, University of Kansa

Abstract:

A new mechanistic deterministic model for assessing the impact of temperature variability on malaria transmission dynamics is developed. The effects of sensitivity and uncertainty in estimates of the parameter values used in numerical simulations of the model are analysed. These analyses reveal that, for temperatures in the range [16-34]°C, the parameters of the model that have the dominant influence on the disease dynamics are the mosquito carrying capacity, transmission probability per contact for susceptible mosquitoes, human recruit- ment rate, mosquito maturation rate, biting rate, transmission probability per contact for susceptible humans, and recovery rate from first-time infections. This study emphasize the combined use of mosquito-reduction strategy and personal protection against mosquito bite during the periods when the mean monthly temperatures are in the range [16.7, 25]°C. For higher daily mean temperatures in the range [26, 34]°C, mosquito-reduction strategy should be emphasized ahead of personal protection. Numerical simulations of the model reveal that mosquito maturation rate has a minimum sensitivity (to the associated reproduction threshold of the model) at T = 24°C and maximum at T = 30°C. The mosquito biting rate has maximum sensitivity at T = 26°C, while the minimum value for the transmission probability per bite for susceptible mosquitoes occurs at T = 24°C. Furthermore, disease burden increases for temperatures between 16°C and 25°C and decreases beyond 25°C. This finding, which supports a recent study by other authors, suggests the importance of the role of global warming on future malaria transmission trends.

Speaker: Devin Willmott

Title: Generative Neural Networks in Semi-Supervised Learning



Abstract: Semi-supervised learning is a relatively new machine learning concept that seeks to use both labeled and unlabeled data to perform supervised learning tasks. We will look at two network types with some promising applications to semi-supervised learning: ladder networks and adversarial networks. For each, we will discuss the motivations behind their architectures & training methods, and derive some favorable theoretical properties about their capabilities.

Title:   Matrix Factorization Techniques for Recommender Systems

Abstract: Recommendation Systems apply Information Retrieval techniques to select the online information relevant to a given user. Collaborative Filtering (CF) is currently most widely used approach to build Recommendation System. To address this issue, the collaborative filtering recommendation algorithm is based on singular value decomposition (SVD) . How the SVD works to make recommendations is presented in this master talk.

Jonathan Proctor will be giving a Master's Talk.  He will be presenting the paper

Learning About When and Where from Imagery

Speaker: Nathan Jacobs, University of Kentucky

Abstract:

Every day billions of images are uploaded to the Internet. Together they provide many high-resolution pictures of the world, from panoramic views of natural landscapes to detailed views of what someone had for dinner. Many are tagged with when and where the picture was taken, thus providing an opportunity to better understand how the appearance of objects and scenes varies with respect to location and time. This talk describes my work in using learning-based methods to extract geo-spatial properties from imagery. In particular, I will focus on two recent research thrusts: using deep convolutional neural networks to geo-calibrate social network imagery and using such imagery to build geo-temporal models of human appearance.

BIO:

Nathan Jacobs earned a PhD in Computer Science at Washington University in St. Louis (2010). Since then, he has been an Assistant Professor of Computer Science at the University of Kentucky. Dr. Jacobs' research area is computer vision; his specialty is developing learning-based algorithms and systems for processing large-scale image collections. His is a recipient of an NSF CAREER award, and his research has been funded by ARMY-SMDC, ARL, DARPA, Google, IARPA, NGA, and NIH. His current focus is on developing techniques for mining information about people and the natural world from geotagged imagery, including images from social networks, publicly available outdoor webcams, and satellites.

Speaker: Luis Sordo Vieira
Title: The benefits of elliptic curve cryptography
Abstract: We will introduce the basis of elliptic curve cryptography. Roughly speaking ECC is based on the group structure of the points defined on an elliptic curve over a finite field and the difficulty of solving the discrete log problem. The applications are many, such as signature verification and pseudo random generators. No knowledge of algebraic geometry is required.